Molecular investigations of marine microbial ecology
Principal Investigators: Chris Scholin, Ed DeLong
A diverse group of microorganisms, from unicellular algae to bacteria and viruses, play integral roles in the cycling of nutrients and other compounds in the ocean. Current methods for identifying microbial species and linking them to specific biogeochemical processes are time consuming and often problematic, hindering scientific pursuits to understand the role microbes play in the environment. For the rapid identification of certain toxic algae, MBARI researchers have devised molecular probes which are being evaluated in many locations around the world. These probes continue to undergo refinements to improve their reliability and make them easier to use. At the same time, the microbial researchers are expanding investigations into the far broader realm of non-toxic species to determine whether a similar genetic-based strategy is viable for pinning down the identity of these other, more prevalent microorganisms. This work could potentially contribute to a much more detailed understanding of marine ecosytems and their biodiversity, as well as improve our understanding of the evolution of marine microorganisms. Over the long term, the goal is to integrate ecological studies of marine microbes with the more broad-scale chemical, biological, and physical oceanographic research of Project 1. For 1998 there are three components in Project 5:
P5A Development and application of DNA probes and novel instrumentation for detection and quantification of toxic and nontoxic phytoplankton Researchers will draw on the findings of MBARIs Monterey Bay time series (under Project 1), which includes data on occurrences of phytoplankton blooms and other microbial populations. They will collect samples of numerous phytoplankton found in Monterey Bay and raise these as pure cultures in the laboratory. Using a variety of molecular biological techniques, they will then determine gene sequences as a means to discriminate between the organisms collected. These methods will reveal a kind of "genetic identity" of the organisms which can then be compared to their traditional taxonomic classification based on cell structure and form. In this fashion it will be possible to link the molecular classifications to existing time-series data as a first step toward understanding the details of what "genetic units" occur with respect to variables such as physical location, season, water temperature, seawater chemical concentrations, etc.
The molecular biologists then hope to utilize the molecular "signatures" to develop probes that could enable rapid identification of major groups of organisms in Monterey Bay. This would allow researchers to obtain much more accurate information on the rise and fall of microbial populations and their links to the rest of the marine food web. If probe development proves possible, the next step would be to devise reliable, low-cost, stand-alone instruments to automate their application at sea.
P5B Development of methods for detection, quantification, and biogeochemical characterization of dominant planktonic prokaryotesMarine prokaryotes (one-celled organisms such as bacteria, which lack a defined nucleus) are known to play central roles in the cycling of carbon, nitrogen, and sulfur. However, few specific details of how microbes carry out their roles are known. Standard microbiological methods have not succeeded in revealing much about the workings of most of the dominant and ecologically important marine microbes, largely because these organisms have been all but impossible to raise in laboratory cultures. A recently developed technique, the application of a "phylogenetic stain"a kind of molecular name taggets around this limitation by allowing researchers to specifically identify and quantify individual microbial cells. This technique, although powerful, currently has severe limitations for broad application in seawater samples. MBARI researchers are improving this method to study and describe the hugely abundant and extremely diverse marine bacteria in the water column and at the seafloor. One group of particular interest, the Archaea, are more closely related to humans than to typical bacteria. Although previously thought to inhabit only extreme environments such as hydrothermal vents, Archaea are now known to thrive in deep waters throughout the world's oceans. Discovered only five years ago, these new Archaea are believed to represent a large fraction of the microbes found below the illuminated zone of the ocean. Even so, the ecology of bacterial populations in the plankton remains poorly described. Taking a census, so to speak, of marine microbes will lay the groundwork for teasing out the details of their roles in biogeochemical processes.
P5C Development of methods for characterizing marine viruses and their effects on co-occurring prokaryotic microorganismsViruses have only recently been recognized as abundant and ubiquitous in ocean waters, and scientific knowledge of marine viruses is virtually in its infancy. Viruses are suspected to be active players in the "microbial loop"a mini ocean food-chain, comprised of decomposing organic matter on its way to the seafloor and populated by scavenger microbes. Another mysterious phenomenon in which viruses are implicated is the sudden crash of phytoplankton populations after an explosive increase, or bloom. It may be that viral infections act to limit the lifespans or productivity of phytoplankton; if so, viruses may impact organisms higher up the food chain. MBARI researchers will develop a new filtration device, for use on ROVs or at the ocean floor, to concentrate viruses in seawater samples. In parallel studies of phytoplankton and bacterioplankton, new molecular methods will be developed to describe and distinguish marine viruses, so that researchers can begin to gauge their ecological importance.
Last updated: 07 October 2004